#include "mzParser.h"
#ifdef MZP_MZ5

mzpMz5Handler::mzpMz5Handler(mzpMz5Config* c, BasicSpectrum* s){
	config_=c;
	spec=s;
}

mzpMz5Handler::mzpMz5Handler(mzpMz5Config* c, BasicSpectrum* s, BasicChromatogram* bc){
	config_=c;
	spec=s;
	chromat=bc;
}

mzpMz5Handler::~mzpMz5Handler(){
	config_=NULL;
	spec=NULL;
	chromat=NULL;
}

void mzpMz5Handler::clean(const MZ5DataSets v, void* data, const size_t dsend) {
    hsize_t dim[1] =
    { static_cast<hsize_t> (dsend) };
    DataSpace dsp(1, dim);
    DataSet::vlenReclaim(data, config_->getDataTypeFor(v), dsp);
    free(data);
    data = 0;
    dsp.close();
}

vector<cMz5Index>* mzpMz5Handler::getChromatIndex(){
	return &m_vChromatIndex;
}

void mzpMz5Handler::getData(vector<double>& data, const MZ5DataSets v, const hsize_t start, const hsize_t end) {
	hsize_t scount = end - start;
	data.resize(scount);
	if (scount > 0) {
		map<MZ5DataSets, DataSet>::iterator it = bufferMap_.find(v);
		if (it == bufferMap_.end()) {
			DataSet ds = file_->openDataSet(config_->getNameFor(v));
			bufferMap_.insert(pair<MZ5DataSets, DataSet>(v, ds));
			it = bufferMap_.find(v);
		}
		DataSet dataset = it->second;
		DataSpace dataspace = dataset.getSpace();
		hsize_t offset[1];
		offset[0] = start;
		hsize_t count[1];
		count[0] = scount;
		dataspace.selectHyperslab(H5S_SELECT_SET, count, offset);

		hsize_t dimsm[1];
		dimsm[0] = scount;
		DataSpace memspace(1, dimsm);

		dataset.read(&data[0], PredType::NATIVE_DOUBLE, memspace, dataspace);

		if (v == SpectrumMZ && config_->doTranslating()) {
			size_t ms = data.size();
			double s = 0;
			for (size_t i = 0; i < ms; ++i) {
				data[i] = data[i] + s;
				s = data[i];
			}
		}
		if (v == SpectrumIntensity && config_->doTranslating()) {
			//there is no translating to do...
			//Translator_mz5::reverseTranslateIntensity(data);
		}
		memspace.close();
		dataspace.close();
	}
}

const map<MZ5DataSets, size_t>& mzpMz5Handler::getFields() {
	return fields_;
}

vector<cMz5Index>* mzpMz5Handler::getSpecIndex(){
	return &m_vIndex;
}

int mzpMz5Handler::highChromat() {
	return m_vChromatIndex.size();
}

int mzpMz5Handler::highScan() {
	if(m_vIndex.size()==0) return 0;
	return m_vIndex[m_vIndex.size()-1].scanNum;
}

int mzpMz5Handler::lowScan() {
	if(m_vIndex.size()==0) return 0;
	return m_vIndex[0].scanNum;
}

void mzpMz5Handler::processCVParams(unsigned long index){
	if(cvRef[cvParams_[index].typeCVRefID].group==0){ //MS:
		switch(cvRef[cvParams_[index].typeCVRefID].ref) {
			case 1000016:
				if(cvRef[cvParams_[index].unitCVRefID].ref==31) spec->setRTime((float)atof(cvParams_[index].value));
				else spec->setRTime((float)atof(cvParams_[index].value)/60.0f); //assume seconds if not minutes
				break;
			case 1000041:
				spec->setPrecursorCharge(atoi(cvParams_[index].value));
				break;
			case 1000042:
				spec->setPrecursorIntensity(atof(cvParams_[index].value));
				break;
			case 1000045:
				spec->setCollisionEnergy(atof(cvParams_[index].value));
				break;
			case 1000127:
				spec->setCentroid(true);
				break;
			case 1000285:
				spec->setTotalIonCurrent(atof(cvParams_[index].value));
				break;
			case 1000504:
				spec->setBasePeakMZ(atof(cvParams_[index].value));
				break;
			case 1000505:
				spec->setBasePeakIntensity(atof(cvParams_[index].value));
				break;
			case 1000511:
				spec->setMSLevel(atoi(cvParams_[index].value));
				break;	
			case 1000512:
				spec->setFilterLine(cvParams_[index].value);
				break;
			case 1000527:
				spec->setHighMZ(atof(cvParams_[index].value));
				break;
			case 1000528:
				spec->setLowMZ(atof(cvParams_[index].value));
				break;
			case 1000744:
				spec->setPrecursorMZ(atof(cvParams_[index].value));
				break;
			default:
				//cout << "Unknown/Unparsed CV: " << cvRef[cvParams_[index].typeCVRefID].group << ":" << cvRef[cvParams_[index].typeCVRefID].ref << endl;
				break;
		}
	} else { //unknown:
		//cout << "Unknown/Unparsed CV: " << cvRef[cvParams_[index].typeCVRefID].group << ":" << cvRef[cvParams_[index].typeCVRefID].ref << endl;
	}

}

bool mzpMz5Handler::readChromatogram(int num){
	if(chromat==NULL) return false;
	chromat->clear();

	//if no chromatogram was requested, grab the next one
	if(num<0)	posChromatIndex++;
	else posChromatIndex=num;
	if(posChromatIndex>=(int)m_vChromatIndex.size()) return false;
	
	//Read the chromatogram
	vector<double> time, inten;
	TimeIntensityPair tip;
	if(posChromatIndex==0){
		getData(time, ChromatogramTime, 0, (hsize_t)m_vChromatIndex[posChromatIndex].offset);
		getData(inten, ChromatogramIntensity, 0, (hsize_t)m_vChromatIndex[posChromatIndex].offset);
	} else {
		getData(time, ChromatogramTime, (hsize_t)m_vChromatIndex[posChromatIndex-1].offset, (hsize_t)m_vChromatIndex[posChromatIndex].offset);
		getData(inten, ChromatogramIntensity, (hsize_t)m_vChromatIndex[posChromatIndex-1].offset, (hsize_t)m_vChromatIndex[posChromatIndex].offset);
	}
	for(unsigned int i=0;i<time.size();i++){
		tip.time=time[i];
		tip.intensity=inten[i];
		chromat->addTIP(tip);
	}

	//Read the metadata
	unsigned long start=m_vChromatIndex[posChromatIndex].cvStart;
	unsigned long stop=start+m_vChromatIndex[posChromatIndex].cvLen;
	for(size_t i=start;i<stop;i++) processCVParams(i);
	chromat->setIDString(&m_vChromatIndex[posChromatIndex].idRef[0]);

	return true;
}

void* mzpMz5Handler::readDataSet(const MZ5DataSets v, size_t& dsend, void* ptr) {
	DataSet ds = file_->openDataSet(config_->getNameFor(v));
	DataSpace dsp = ds.getSpace();
	hsize_t start[1], end[1];
	dsp.getSelectBounds(start, end);
	dsend = (static_cast<size_t> (end[0])) + 1;
	DataType dt = config_->getDataTypeFor(v);
	if (ptr == 0) ptr = calloc(dsend, dt.getSize());
	ds.read(ptr, dt);
	dsp.close();
	ds.close();
	return ptr;
}

bool mzpMz5Handler::readFile(const string filename){

	FileCreatPropList fcparm = FileCreatPropList::DEFAULT;
	FileAccPropList faparm = FileAccPropList::DEFAULT;

	int mds_nelemts;
	size_t rdcc_nelmts, rdcc_nbytes;
	double rdcc_w0;
	faparm.getCache(mds_nelemts, rdcc_nelmts, rdcc_nbytes, rdcc_w0);
	//TODO do not set global buffer size, instead set dataset specific buffer size
	rdcc_nbytes = config_->getBufferInB();
	//TODO can be set to 1 if chunks that have been fully read/written will never be read/written again
	//rdcc_w0 = 1.0;
	rdcc_nelmts = config_->getRdccSlots();
	faparm.setCache(mds_nelemts, rdcc_nelmts, rdcc_nbytes, rdcc_w0);

	try {
		file_ = new H5File(filename, H5F_ACC_RDONLY, fcparm, faparm);
	} catch (FileIException&){
		return false;
	}
	closed_ = false;

	hsize_t start[1], end[1];
	size_t dsend = 0;
	DataSet dataset;
	DataSpace dataspace;
	string oname;
	MZ5DataSets v;
	for (hsize_t i = 0; i < file_->getNumObjs(); ++i) {
		oname = file_->getObjnameByIdx(i);
		dataset = file_->openDataSet(oname);
		dataspace = dataset.getSpace();
		dataspace.getSelectBounds(start, end);
		dsend = (static_cast<size_t> (end[0])) + 1;
		try {
			v = config_->getVariableFor(oname);
			fields_.insert(pair<MZ5DataSets, size_t>(v, dsend));
		} catch (out_of_range&) {
		}
		dataspace.close();
		dataset.close();
	}

	map<MZ5DataSets, size_t>::const_iterator it;
	it = fields_.find(FileInformation);
	if (it != fields_.end()) {
		DataSet ds = file_->openDataSet(config_->getNameFor(FileInformation));
		DataSpace dsp = ds.getSpace();
		hsize_t start[1], end[1];
		dsp.getSelectBounds(start, end);
		dsend = (static_cast<size_t> (end[0])) + 1;
		DataType dt = config_->getDataTypeFor(FileInformation);
		FileInformationMZ5* fi = (FileInformationMZ5*) (calloc(dsend, dt.getSize()));
		ds.read(fi, dt);
		dsp.close();
		ds.close();

		if (dsend == 1) {
			if (fi[0].majorVersion == MZ5_FILE_MAJOR_VERSION && fi[0].minorVersion == MZ5_FILE_MINOR_VERSION) {
				config_->setFiltering(fi[0].didFiltering > 0 ? true : false);
				config_->setTranslating(fi[0].deltaMZ && fi[0].translateInten);
			}
		}
		
		hsize_t dim[1] = { static_cast<hsize_t> (dsend) };
		DataSpace dspr(1, dim);
		DataSet::vlenReclaim(fi, config_->getDataTypeFor(FileInformation), dspr);
		free(fi);
		fi = 0;
		dspr.close();
	} else {
		it = fields_.find(Run);
		if (it == fields_.end()) {
			throw runtime_error("mzpMz5Handler::readFile(): given file is not mz5.");
			return false;
		}
	}

	//Read the CV Reference List
	size_t numberOfRef = fields_.find(CVReference)->second;
	CVRefMZ5* cvrl = (CVRefMZ5*) readDataSet(CVReference, dsend);
	cvRef.clear();
	CVRefItem cvr;
	for(int xx=0;xx<numberOfRef;xx++){
		if(strcmp(cvrl[xx].prefix,"MS")==0) cvr.group=0;
		else if(strcmp(cvrl[xx].prefix,"UO")==0) cvr.group=1;
		else cvr.group=2;
		cvr.ref=cvrl[xx].accession;
		cvRef.push_back(cvr);
		//cout << cvrl[xx].name << "\t" << cvrl[xx].prefix << ":" << cvrl[xx].accession << endl;
	}
	clean(CVReference, cvrl, dsend);
	
	//Read the CVParams
	size_t numberOfCV = fields_.find(CVParam)->second;
	cvParams_.resize(numberOfCV);
	readDataSet(CVParam, dsend, &cvParams_[0]);

	//Build the index
	m_vIndex.clear();
	m_scanIDXCount=0;
	size_t numberOfSpectra_ = fields_.find(SpectrumMetaData)->second;
	vector<unsigned long> index;
	index.resize(numberOfSpectra_);
	readDataSet(SpectrumIndex,dsend,&index[0]);
	
	BinaryDataMZ5* binaryParamsData_ = (BinaryDataMZ5*) calloc(numberOfSpectra_, sizeof(BinaryDataMZ5));
	readDataSet(SpectrumBinaryMetaData, dsend, binaryParamsData_);

	SpectrumMZ5* spectrumData_ = (SpectrumMZ5*) calloc(numberOfSpectra_, sizeof(SpectrumMZ5));
	readDataSet(SpectrumMetaData, dsend, spectrumData_);
	
	for(size_t i=0;i<dsend;i++){
		/*
		if(i==0 || i==3237 || i==3238 || i==3239){
			cout << i << "\t" << spectrumData_[i].precursorList.len << endl;
			cout << i << "\t" << spectrumData_[i].paramList.cvParamStartID << "\t" << spectrumData_[i].paramList.cvParamEndID << endl;
			for(size_t j=spectrumData_[i].paramList.cvParamStartID;j<binaryParamsData_[i].xParamList.cvParamEndID;j++){
				cout << cvParams_[j].typeCVRefID << "\t" << cvParams_[j].unitCVRefID << "\t" << cvParams_[j].value << endl;
			}
			cout << i << "\t" << binaryParamsData_[i].xParamList.cvParamStartID << "\t" << binaryParamsData_[i].xParamList.cvParamEndID << endl;
			cout << i << "\t" << binaryParamsData_[i].yParamList.cvParamStartID << "\t" << binaryParamsData_[i].yParamList.cvParamEndID << endl;
			cout << endl;
		}
		*/
		curIndex.cvStart=spectrumData_[i].paramList.cvParamStartID;
		curIndex.cvLen=binaryParamsData_[i].xParamList.cvParamEndID-curIndex.cvStart;
		curIndex.idRef=spectrumData_[i].id;
		curIndex.offset=index[i];
		if(strstr(&curIndex.idRef[0],"scan=")!=NULL)	{
			curIndex.scanNum=atoi(strstr(&curIndex.idRef[0],"scan=")+5);
		} else if(strstr(&curIndex.idRef[0],"scanId=")!=NULL) {
			curIndex.scanNum=atoi(strstr(&curIndex.idRef[0],"scanId=")+7);
		} else if(strstr(&curIndex.idRef[0],"S")!=NULL) {
			curIndex.scanNum=atoi(strstr(&curIndex.idRef[0],"S")+1);
		} else {
			curIndex.scanNum=++m_scanIDXCount;
		}
		m_vIndex.push_back(curIndex);
	}

	//Build the chromatogram index
	m_vChromatIndex.clear();
	size_t numberOfChromats_ = fields_.find(ChromatogramMetaData)->second;
	index.clear();
	index.resize(numberOfChromats_);
	readDataSet(ChromatogramIndex,dsend,&index[0]);
	
	free(binaryParamsData_);
	binaryParamsData_ = (BinaryDataMZ5*) calloc(numberOfChromats_, sizeof(BinaryDataMZ5));
	readDataSet(ChromatogramBinaryMetaData, dsend, binaryParamsData_);

	ChromatogramMZ5* chromatogramData_ = (ChromatogramMZ5*) calloc(numberOfSpectra_, sizeof(ChromatogramMZ5));
	readDataSet(ChromatogramMetaData, dsend, chromatogramData_);
	
	for(size_t i=0;i<dsend;i++){
		/*
		if(i==0 || i==3237 || i==3238 || i==3239){
			cout << i << "\t" << spectrumData_[i].precursorList.len << endl;
			cout << i << "\t" << spectrumData_[i].paramList.cvParamStartID << "\t" << spectrumData_[i].paramList.cvParamEndID << endl;
			for(size_t j=spectrumData_[i].paramList.cvParamStartID;j<binaryParamsData_[i].xParamList.cvParamEndID;j++){
				cout << cvParams_[j].typeCVRefID << "\t" << cvParams_[j].unitCVRefID << "\t" << cvParams_[j].value << endl;
			}
			cout << i << "\t" << binaryParamsData_[i].xParamList.cvParamStartID << "\t" << binaryParamsData_[i].xParamList.cvParamEndID << endl;
			cout << i << "\t" << binaryParamsData_[i].yParamList.cvParamStartID << "\t" << binaryParamsData_[i].yParamList.cvParamEndID << endl;
			cout << endl;
		}
		*/
		curChromatIndex.cvStart=chromatogramData_[i].paramList.cvParamStartID;
		curChromatIndex.cvLen=binaryParamsData_[i].xParamList.cvParamEndID-curChromatIndex.cvStart;
		curChromatIndex.idRef=chromatogramData_[i].id;
		curChromatIndex.offset=index[i];
		m_vChromatIndex.push_back(curChromatIndex);
	}

	free(spectrumData_);
	free(chromatogramData_);
	free(binaryParamsData_);

	posIndex=-1;
	posChromatIndex=-1;

	return true;

}

bool mzpMz5Handler::readHeader(int num){
	spec->clear();

	//if no scan was requested, grab the next one
	if(num<0){
		posIndex++;
		if(posIndex>=(int)m_vIndex.size()) return false;
	} else { //otherwise do binary search for scan number
		//Assumes scan numbers are in order
		int mid=m_vIndex.size()/2;
		int upper=m_vIndex.size();
		int lower=0;
		while(m_vIndex[mid].scanNum!=num){
			if(lower==upper) break;
			if(m_vIndex[mid].scanNum>num){
				upper=mid-1;
				mid=(lower+upper)/2;
			} else {
				lower=mid+1;
				mid=(lower+upper)/2;
			}
		}
		if(m_vIndex[mid].scanNum==num) posIndex=mid;
	}

	//Read the metadata
	unsigned long start=m_vIndex[posIndex].cvStart;
	unsigned long stop=start+m_vIndex[posIndex].cvLen;
	for(size_t i=start;i<stop;i++) processCVParams(i);

	//Get the peak count - this wastes time, though
	vector<double> mz;
	if(posIndex==0) getData(mz, SpectrumMZ, 0, (hsize_t)m_vIndex[posIndex].offset);
	else getData(mz, SpectrumMZ, (hsize_t)m_vIndex[posIndex-1].offset, (hsize_t)m_vIndex[posIndex].offset);
	spec->setPeaksCount((int)mz.size());

	if(spec->getScanNum()!=m_vIndex[posIndex].scanNum) spec->setScanNum(m_vIndex[posIndex].scanNum);
	spec->setScanIndex(posIndex+1); //set the index, which starts from 1, so offset by 1

	return true;

}

bool mzpMz5Handler::readSpectrum(int num){
	spec->clear();

	//if no scan was requested, grab the next one
	if(num<0){
		posIndex++;
		if(posIndex>=(int)m_vIndex.size()) return false;
	} else { //otherwise do binary search for scan number
		//Assumes scan numbers are in order
		int mid=m_vIndex.size()/2;
		int upper=m_vIndex.size();
		int lower=0;
		while(m_vIndex[mid].scanNum!=num){
			if(lower==upper) break;
			if(m_vIndex[mid].scanNum>num){
				upper=mid-1;
				mid=(lower+upper)/2;
			} else {
				lower=mid+1;
				mid=(lower+upper)/2;
			}
		}
		if(m_vIndex[mid].scanNum==num) posIndex=mid;
	}

	//Read the peaks
	vector<double> mz, inten;
	specDP dp;
	if(posIndex==0){
		getData(mz, SpectrumMZ, 0, (hsize_t)m_vIndex[posIndex].offset);
		getData(inten, SpectrumIntensity, 0, (hsize_t)m_vIndex[posIndex].offset);
	} else {
		getData(mz, SpectrumMZ, (hsize_t)m_vIndex[posIndex-1].offset, (hsize_t)m_vIndex[posIndex].offset);
		getData(inten, SpectrumIntensity, (hsize_t)m_vIndex[posIndex-1].offset, (hsize_t)m_vIndex[posIndex].offset);
	}
	for(unsigned int i=0;i<mz.size();i++){
		dp.mz=mz[i];
		dp.intensity=inten[i];
		spec->addDP(dp);
	}
	spec->setPeaksCount((int)mz.size());

	//Read the metadata
	unsigned long start=m_vIndex[posIndex].cvStart;
	unsigned long stop=start+m_vIndex[posIndex].cvLen;
	for(size_t i=start;i<stop;i++) processCVParams(i);

	if(spec->getScanNum()!=m_vIndex[posIndex].scanNum) spec->setScanNum(m_vIndex[posIndex].scanNum);
	spec->setScanIndex(posIndex+1); //set the index, which starts from 1, so offset by 1

	return true;

}

#endif
